HGG Advances最新文献

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GWAS and multi-omics integrative analysis reveal novel loci and their molecular mechanisms for circulating fatty acids. 全基因组关联研究和多组学整合分析揭示了循环多不饱和脂肪酸、单不饱和脂肪酸和饱和脂肪酸的新位点及其分子机制。
IF 3.6
HGG Advances Pub Date : 2025-10-09 Epub Date: 2025-06-21 DOI: 10.1016/j.xhgg.2025.100470
Yitang Sun, Huifang Xu, Kaixiong Ye
{"title":"GWAS and multi-omics integrative analysis reveal novel loci and their molecular mechanisms for circulating fatty acids.","authors":"Yitang Sun, Huifang Xu, Kaixiong Ye","doi":"10.1016/j.xhgg.2025.100470","DOIUrl":"10.1016/j.xhgg.2025.100470","url":null,"abstract":"<p><p>Previous genome-wide association studies (GWAS) have identified genetic loci associated with the circulating levels of fatty acids (FAs), but the biological mechanisms of these genetic associations remain largely unexplored. Here, we conducted GWAS to identify additional genetic loci for 19 circulating FA traits in UK Biobank participants of European ancestry (n = 239,268) and five other ancestries (n = 508-4,663). We leveraged the GWAS findings to characterize genetic correlations and colocalized regions among FAs, explore sex differences, examine FA loci influenced by lipoprotein metabolism, and apply statistical fine-mapping to pinpoint putative causal variants. We integrated GWAS signals with multi-omics quantitative trait loci (QTL) to reveal intermediate molecular phenotypes mediating the associations between the genetic loci and FA levels. We identified 215 genome-wide significant, independent loci for polyunsaturated fatty acid (PUFA)-related traits in European participants, 163 loci for monounsaturated fatty acid (MUFA)-related traits, and 119 loci for saturated fatty acid (SFA)-related traits, including 70, 61, and 54 novel loci, respectively. A novel locus for total FAs, the percentage of omega-6 PUFAs in total FAs, and total MUFAs (around genes GSTT1/2/2B) colocalized with QTL signals for all six molecular phenotypes examined, including gene expression, protein abundance, DNA methylation, splicing, histone modification, and chromatin accessibility. Across 19 FA traits, 35% of GWAS loci colocalized with QTL signals for at least one molecular phenotype. Our study identifies novel genetic loci for circulating FA levels and systematically uncovers their underlying molecular mechanisms.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100470"},"PeriodicalIF":3.6,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12272887/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144369236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genotyping TOMM40'523 poly-T polymorphisms using whole-genome sequencing. 利用全基因组测序对TOMM40'523多态性进行基因分型
IF 3.6
HGG Advances Pub Date : 2025-10-09 Epub Date: 2025-08-07 DOI: 10.1016/j.xhgg.2025.100488
Ricardo A Vialle, Lei Yu, Yan Li, Roberto T Raittz, Jose M Farfel, Philip L De Jager, Julie A Schneider, Lisa L Barnes, Shinya Tasaki, David A Bennett
{"title":"Genotyping TOMM40'523 poly-T polymorphisms using whole-genome sequencing.","authors":"Ricardo A Vialle, Lei Yu, Yan Li, Roberto T Raittz, Jose M Farfel, Philip L De Jager, Julie A Schneider, Lisa L Barnes, Shinya Tasaki, David A Bennett","doi":"10.1016/j.xhgg.2025.100488","DOIUrl":"10.1016/j.xhgg.2025.100488","url":null,"abstract":"<p><p>The TOMM40'523 poly-T repeat polymorphism (rs10524523) has been associated with cognitive decline and Alzheimer's disease (AD) progression. Challenges in processing whole-genome sequencing (WGS) data traditionally require additional PCR and targeted sequencing assays to genotype these polymorphisms. We introduce a computational pipeline that integrates multiple short tandem repeat (STR) detection tools in an ensemble machine learning model using XGBoost. Using a sample of 1,202 participants from 4 cohort studies, we benchmarked our method against PCR-based measures. Our ensemble model outperformed individual STR tools, improving repeat length estimation accuracy (R<sup>2</sup> = 0.92) and achieving an accuracy rate of 93.2% compared with PCR-derived genotypes. Additionally, we validated our WGS-derived genotypes by replicating previously reported associations between TOMM40'523 variants and cognitive decline. Our computational genotyping tool is a scalable and reliable alternative to PCR-based assays, enabling broader investigations of TOMM40 variation in studies with WGS data.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100488"},"PeriodicalIF":3.6,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144805011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Modeling MPPH syndrome in vivo using Breasi-CRISPR. 使用Breasi-CRISPR在体内建立MPPH综合征模型。
IF 3.6
HGG Advances Pub Date : 2025-10-09 Epub Date: 2025-08-23 DOI: 10.1016/j.xhgg.2025.100497
Claire M Kittock, Krishna Karia, Pratiksha Kc, Claire Evans, Jared Wollman, Brandon L Meyerink, Louis-Jan Pilaz
{"title":"Modeling MPPH syndrome in vivo using Breasi-CRISPR.","authors":"Claire M Kittock, Krishna Karia, Pratiksha Kc, Claire Evans, Jared Wollman, Brandon L Meyerink, Louis-Jan Pilaz","doi":"10.1016/j.xhgg.2025.100497","DOIUrl":"10.1016/j.xhgg.2025.100497","url":null,"abstract":"<p><p>The increasing availability and affordability of genetic testing has resulted in the identification of numerous novel variants associated with neurodevelopmental disorders. There remains a need for methods to analyze the functional impact of these variants. Some methods, like expressing these variants in cell culture, may be rapid, but they lack physiologic context. Other methods, like making a whole-mouse model, may provide physiologic accuracy, but these are costly and time-consuming. We recently developed a technique, Breasi-CRISPR (Brain Easi-CRISPR), which results in efficient genome editing of neural precursor cells via electroporation of CRISPR-Cas9 reagents into developing mouse brains. Since Breasi-CRISPR is extremely rapid and enables the analysis of targeted genes in vivo, we wondered whether this technique would accelerate the study of monogenic neurodevelopmental disorders. Here, we use Breasi-CRISPR to model megalencephaly postaxial polydactyly polymicrogyria hydrocephalus (MPPH) syndrome. We found that 2 days after Breasi-CRISPR, we were able to see neurodevelopmental phenotypes known to be associated with MPPH syndrome, including increased cyclin D2 protein abundance and an increase in neural progenitor proliferation. Thus, Breasi-CRISPR can efficiently model MPPH syndrome and may be a powerful method to add to the toolbox of those investigating the functional impact of patient variants in neurodevelopmental disorders.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100497"},"PeriodicalIF":3.6,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12447981/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144972063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Characteristics predicting reduced penetrance variants in the high-risk cancer predisposition gene TP53. 预测高风险癌症易感性基因TP53外显率降低变异的特征。
IF 3.6
HGG Advances Pub Date : 2025-10-09 Epub Date: 2025-07-21 DOI: 10.1016/j.xhgg.2025.100484
Cristina Fortuno, Marcy E Richardson, Tina Pesaran, Kelly McGoldrick, Paul A James, Amanda B Spurdle
{"title":"Characteristics predicting reduced penetrance variants in the high-risk cancer predisposition gene TP53.","authors":"Cristina Fortuno, Marcy E Richardson, Tina Pesaran, Kelly McGoldrick, Paul A James, Amanda B Spurdle","doi":"10.1016/j.xhgg.2025.100484","DOIUrl":"10.1016/j.xhgg.2025.100484","url":null,"abstract":"<p><p>Disease-causing variants with penetrance that is lower than the average expected for a given gene complicate classification, even when using gene-specific guidelines. For TP53, a gene associated with some of the highest cancer risks, even reduced penetrance disease-predisposition variants remain clinically actionable. We conducted a review of ClinVar submissions to identify TP53 variants flagged as having reduced penetrance by genetic testing laboratories and analyzed functional, bioinformatic, immunogenicity, frequency, and clinical features of these variants compared with standard pathogenic and benign variants. Our findings show that reported reduced penetrance TP53 variants are more likely to exhibit intermediate functional activity in multiple assays and are predicted as deleterious with bioinformatic tools, though with lower scores than pathogenic variants. These variants also have a higher population frequency than pathogenic variants, and heterozygotes tend to manifest disease later in life, suggesting a need for refined clinical criteria to better capture attenuated Li-Fraumeni syndrome phenotypes. Finally, by applying a random forest prediction model to all TP53 uncertain or conflicting variants in ClinVar, we identified 106 additional variants with potential reduced penetrance.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100484"},"PeriodicalIF":3.6,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12337872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144691810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Expanding implementation of pediatric whole-genome sequencing: Insights from SeqFirst providers to inform equitable access to a precise genetic diagnosis. 扩大儿科全基因组测序的实施:来自SeqFirst提供者的见解,为公平获得精确的遗传诊断提供信息。
IF 3.6
HGG Advances Pub Date : 2025-10-09 Epub Date: 2025-06-03 DOI: 10.1016/j.xhgg.2025.100464
Joon-Ho Yu, Katherine E MacDuffie, Olivia Sommerland, Tesla Theoryn, Priyanka Murali, Kailyn Anderson, Megan Sikes, Lukas Kruidenier, Heidi I S Gildersleeve, Abbey Scott, Kati J Buckingham, Kirsty McWalter, Paul Kruszka, Alexandra C Keefe, Jessica X Chong, David L Veenstra, Katrina M Dipple, Tara Wenger, Dan Doherty, Michael J Bamshad
{"title":"Expanding implementation of pediatric whole-genome sequencing: Insights from SeqFirst providers to inform equitable access to a precise genetic diagnosis.","authors":"Joon-Ho Yu, Katherine E MacDuffie, Olivia Sommerland, Tesla Theoryn, Priyanka Murali, Kailyn Anderson, Megan Sikes, Lukas Kruidenier, Heidi I S Gildersleeve, Abbey Scott, Kati J Buckingham, Kirsty McWalter, Paul Kruszka, Alexandra C Keefe, Jessica X Chong, David L Veenstra, Katrina M Dipple, Tara Wenger, Dan Doherty, Michael J Bamshad","doi":"10.1016/j.xhgg.2025.100464","DOIUrl":"10.1016/j.xhgg.2025.100464","url":null,"abstract":"<p><p>Whole-genome sequencing (WGS) as a diagnostic test offers children suspected of having a rare genetic condition and their families the best direct path toward securing a precise genetic diagnosis (PrGD). Yet, a limited supply and inequitable access to genetic services are impediments to realizing the benefits of a PrGD. Such access disparities might be due to a range of structural and social determinants that manifest in interactions, or the lack thereof, between families, providers, and institutions. Semi-structured key informant interviews (n = 19) were conducted with neonatologists and neurodevelopmental clinic providers (NDV providers) who referred families to the SeqFirst study to identify barriers and inform strategies to improve equitable access to a PrGD via WGS. Overall, neonatologists and NDV providers were enthusiastic about offering WGS to their patients and families despite different contexts of medical care. Providers cited several considerations that influenced their introduction of WGS and genetic testing to families, including their perceptions of families' capacity, readiness, and distrust and the establishment of sufficient provider-family rapport. These considerations influenced providers' timing and introduction of genetic testing and WGS to families. Together, these findings suggest that providers' perceptions of families may result in delayed introduction of WGS.‬ Despite enthusiasm for early WGS across medical subspecialties, providers' perceptions of families and their social contexts highlight both challenges and opportunities in the implementation of WGS to promote and maximize equitable access.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100464"},"PeriodicalIF":3.6,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12357158/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144226965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A specialized reference panel with structural variants integration for improving genotype imputation in Alzheimer disease and related dementias. 一个专门的参考小组与结构变异整合,以改善阿尔茨海默病和相关痴呆(ADRD)的基因型Imputation。
IF 3.6
HGG Advances Pub Date : 2025-10-09 Epub Date: 2025-07-31 DOI: 10.1016/j.xhgg.2025.100487
Po-Liang Cheng, Hui Wang, Beth A Dombroski, John J Farrell, Iris Horng, Tingting Chung, Giuseppe Tosto, Brian W Kunkle, William S Bush, Badri Vardarajan, Gerard D Schellenberg, Wan-Ping Lee
{"title":"A specialized reference panel with structural variants integration for improving genotype imputation in Alzheimer disease and related dementias.","authors":"Po-Liang Cheng, Hui Wang, Beth A Dombroski, John J Farrell, Iris Horng, Tingting Chung, Giuseppe Tosto, Brian W Kunkle, William S Bush, Badri Vardarajan, Gerard D Schellenberg, Wan-Ping Lee","doi":"10.1016/j.xhgg.2025.100487","DOIUrl":"10.1016/j.xhgg.2025.100487","url":null,"abstract":"<p><p>We developed an imputation panel for Alzheimer disease (AD) and related dementias (ADRD) using 15,958 whole-genome sequencing (WGS) samples from the Alzheimer Disease Sequencing Project. Recognizing the importance of associations between structural variants (SVs) and AD and their underrepresentation in existing public reference panels, our panel uniquely integrates single-nucleotide variants (SNVs), short insertions or deletions (indels), and SVs. This panel enhances the imputation of rare variants underlying disease susceptibility onto genotype array data, offering a cost-effective alternative to WGS while significantly augmenting statistical power. Notably, we discovered 10 rare indels nominally significantly associated with AD that are absent in the TOPMed-r2 panel and identified one genome-wide significant (p < 5 × 10<sup>-8</sup>) and three suggestive significant (p < 1 × 10<sup>-5</sup>) AD-associated SVs. These findings provide the other insights into AD genetics and underscore the critical role of imputation panels in advancing our understanding of complex diseases like ADRD.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100487"},"PeriodicalIF":3.6,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12362095/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144765601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genotypic, functional, and phenotypic characterization in CTNNB1 neurodevelopmental syndrome. CTNNB1神经发育综合征的基因型、功能和表型特征。
IF 3.6
HGG Advances Pub Date : 2025-10-09 Epub Date: 2025-07-18 DOI: 10.1016/j.xhgg.2025.100483
Nina Žakelj, David Gosar, Špela Miroševič, Stephan J Sanders, Alicia Ljungdahl, Sayeh Kohani, Shouhe Huang, Lok I Leong, Ying An, Miou-Jing Teo, Fiona Moultrie, Roman Jerala, Duško Lainšček, Vida Forstnerič, Petra Sušjan, Leszek Lisowski, Andrea Perez-Iturralde, Jasna Oražem Mrak, Ho Yin Edwin Chan, Damjan Osredkar
{"title":"Genotypic, functional, and phenotypic characterization in CTNNB1 neurodevelopmental syndrome.","authors":"Nina Žakelj, David Gosar, Špela Miroševič, Stephan J Sanders, Alicia Ljungdahl, Sayeh Kohani, Shouhe Huang, Lok I Leong, Ying An, Miou-Jing Teo, Fiona Moultrie, Roman Jerala, Duško Lainšček, Vida Forstnerič, Petra Sušjan, Leszek Lisowski, Andrea Perez-Iturralde, Jasna Oražem Mrak, Ho Yin Edwin Chan, Damjan Osredkar","doi":"10.1016/j.xhgg.2025.100483","DOIUrl":"10.1016/j.xhgg.2025.100483","url":null,"abstract":"<p><p>CTNNB1 neurodevelopmental syndrome is a rare disorder caused by de novo heterozygous variants in the CTNNB1 gene encoding β-catenin. This study aimed to characterize genetic variants in individuals with CTNNB1 neurodevelopmental syndrome, systematically assess the spectrum of clinical phenotypes using standardized measures, and explore potential genotype-phenotype correlations. In this cross-sectional cohort study, individuals diagnosed with CTNNB1 neurodevelopmental syndrome underwent structured interviews using standardized scales to evaluate motor skills, speech, communication, feeding abilities, visual function, neurodevelopment, and psychopathology. Genetic variants were analyzed, and, in a subset of cases, the impact of β-catenin variants on the Wnt/β-catenin signaling pathway was assessed. Across the 127 included participants (mean age, 70 months; range, 7-242 months) from 20 countries, we identified 88 different variants of the CTNNB1 gene, 87 of which were predicted to lead to loss of CTNNB1 function. Functional assays demonstrated reduced Wnt signaling activity, including 11 variants that also exhibited a dominant-negative effect. One missense variant demonstrated a gain-of-function effect. Dominant-negative variants were not clearly associated with a distinct phenotype; however, those with missense variants presented a milder phenotype, including earlier achievement of independent walking, fewer motor impairments, better conceptual and social skills, improved communication, and fewer feeding difficulties. This study describes the genetic, functional, and phenotypic characteristics in individuals with CTNNB1 neurodevelopmental syndrome. Further investigation into the genotypic and phenotypic characteristics of this syndrome and their interrelationships is essential to deepen our understanding of the disorder and inform the development of targeted therapies.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100483"},"PeriodicalIF":3.6,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12335994/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genetic rare disease prevention and control: Family-based screening and reproductive interventions in Changsha. 长沙市遗传性罕见病防控:家庭筛查与生殖干预
IF 3.6
HGG Advances Pub Date : 2025-10-09 Epub Date: 2025-08-18 DOI: 10.1016/j.xhgg.2025.100496
Ge Lin, Jun He, Yuankun Wang, Xiangyan Liu, Juan Du, Qianjun Zhang, Shihao Zhou, Lanping Hu, Jing He, Xiurong Li, Hao Hu, Liang Hu, Changgao Zhong, Wen-Bin He, Chan Peng, Zhen Xu, Jingjing Zhang, Yan Shu, Xuan Song, Wenqian Zhang, Guangxiu Lu, Zhiming Ou, Yue-Qiu Tan, Jiyang Liu
{"title":"Genetic rare disease prevention and control: Family-based screening and reproductive interventions in Changsha.","authors":"Ge Lin, Jun He, Yuankun Wang, Xiangyan Liu, Juan Du, Qianjun Zhang, Shihao Zhou, Lanping Hu, Jing He, Xiurong Li, Hao Hu, Liang Hu, Changgao Zhong, Wen-Bin He, Chan Peng, Zhen Xu, Jingjing Zhang, Yan Shu, Xuan Song, Wenqian Zhang, Guangxiu Lu, Zhiming Ou, Yue-Qiu Tan, Jiyang Liu","doi":"10.1016/j.xhgg.2025.100496","DOIUrl":"10.1016/j.xhgg.2025.100496","url":null,"abstract":"<p><p>Rare diseases pose a significant public health challenge, particularly in underserved regions such as China, where genomic diagnostic services and post-diagnosis management remain limited. This study assessed the effectiveness of a rare disease screening program in Changsha, China, which enrolled 85,391 couples between January 2022 and June 2023. Among these participants were 1,414 suspected high-risk couples undergoing genetic testing, with 562 found to be at high risk of having a child with a rare disease, yielding a positive rate of 39.75%. Reproductive interventions were implemented for 319 families, successfully preventing rare disease-affected births in 141 cases. Diagnostic findings informed reproductive decision-making in 25.09% of cases and altered fertility plans in 32.74%. Machine learning analysis further revealed that participation in a parent-offspring trio and a positive family history significantly increased diagnostic likelihood, while singleton recruitment and a negative history were associated with lower diagnostic success. This pilot program highlights the value of integrating genetic diagnostics with reproductive interventions, offering a replicable model for rare disease prevention and management.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100496"},"PeriodicalIF":3.6,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12424409/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144883817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Investigating the role of neighborhood socioeconomic status and germline genetics on prostate cancer risk. 研究邻里社会经济地位和生殖系遗传学在前列腺癌风险中的作用。
IF 3.6
HGG Advances Pub Date : 2025-10-09 Epub Date: 2025-08-08 DOI: 10.1016/j.xhgg.2025.100492
Jonathan Judd, Jeffrey P Spence, Jonathan K Pritchard, Linda Kachuri, John S Witte
{"title":"Investigating the role of neighborhood socioeconomic status and germline genetics on prostate cancer risk.","authors":"Jonathan Judd, Jeffrey P Spence, Jonathan K Pritchard, Linda Kachuri, John S Witte","doi":"10.1016/j.xhgg.2025.100492","DOIUrl":"10.1016/j.xhgg.2025.100492","url":null,"abstract":"<p><p>Genetic factors play an important role in prostate cancer (PCa) development with polygenic risk scores (PRS) predicting disease risk across genetic ancestries. However, there are few convincing modifiable factors for PCa and little is known about their potential interaction with genetic risk. Our study explores the role of neighborhood socioeconomic status (nSES)-and how it may interact with PRS-on PCa risk. We analyzed incident PCa cases and controls of European (cases = 5,960; controls = 93,990) and African (cases = 109; controls = 1,226) ancestry from the UK Biobank cohort. Using the English indices of deprivation, a set of validated metrics that quantify lack of resources within geographical areas, we performed logistic regression to investigate the main effects and interactions between nSES deprivation and genetic susceptibility to PCa, represented by a multi-ancestry PRS comprised of 269 genetic variants. The PRS was associated with PCa in the European (OR = 2.04; 95% confidence interval [CI], 2.00-2.09; p = 5.34 × 10<sup>-807</sup>) and African (OR = 1.35; 95% CI, 1.16-1.58; p = 1.05 × 10<sup>-4</sup>) ancestries. Additionally, nSES deprivation indices were inversely associated with PCa: employment, education, health, and income. From this, we suspect that PRS, through biological mechanisms, and nSES deprivation, likely through differences in screening, are associated with PCa, but act independently of each other. Our findings suggest that genetic factors and social determinants of health measured by neighborhood socioeconomic status do not synergistically increase risk of PCa.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100492"},"PeriodicalIF":3.6,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144812537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comprehensive genotype-phenotype analysis in POLR3-related disorders. polr3相关疾病的综合基因型-表型分析。
IF 3.6
HGG Advances Pub Date : 2025-10-09 Epub Date: 2025-07-18 DOI: 10.1016/j.xhgg.2025.100481
Mackenzie A Michell-Robinson, Stefanie Perrier, Samuel Gauthier, Alexa Derksen, Quentin Sabbagh, Mathias Girbig, Agata D Misiaszek, Amy M Pizzino, Deborah L Renaud, Danilo De Assis Pereira, Paola Okuda, Luciana Maestri Karoleska, Stephanie Keller, Karen Chong, Laurence Gauquelin, Bernard Brais, Barbara Leube, Tiffany Grider, Michael E Shy, Rebecca Schüle, Martina Minnerop, Enrico Bertini, Francesco Nicita, Davide Tonduti, Christoph W Müller, Adeline Vanderver, Nicole I Wolf, Geneviève Bernard
{"title":"Comprehensive genotype-phenotype analysis in POLR3-related disorders.","authors":"Mackenzie A Michell-Robinson, Stefanie Perrier, Samuel Gauthier, Alexa Derksen, Quentin Sabbagh, Mathias Girbig, Agata D Misiaszek, Amy M Pizzino, Deborah L Renaud, Danilo De Assis Pereira, Paola Okuda, Luciana Maestri Karoleska, Stephanie Keller, Karen Chong, Laurence Gauquelin, Bernard Brais, Barbara Leube, Tiffany Grider, Michael E Shy, Rebecca Schüle, Martina Minnerop, Enrico Bertini, Francesco Nicita, Davide Tonduti, Christoph W Müller, Adeline Vanderver, Nicole I Wolf, Geneviève Bernard","doi":"10.1016/j.xhgg.2025.100481","DOIUrl":"10.1016/j.xhgg.2025.100481","url":null,"abstract":"<p><p>RNA polymerase III (RNA Pol III)-related disorders (POLR3-RDs) are a group of clinical entities characterized by causal variants in genes encoding RNA Pol III subunits, including POLR3A, POLR3B, POLR1C, POLR1D, POLR3D, POLR3E, POLR3F, POLR3GL, POLR3H, and POLR3K. These typically cause developmental phenotypes affecting the central nervous system; the eyes; connective tissues including bones, teeth, and endocrine axes; and the reproductive system. Similar phenotypes can be caused by variants in separate subunit genes (multigenic). In contrast, variants in the same gene can cause different phenotypes (pleiotropy), making genotype-phenotype correlation challenging. POLR3-RDs, though individually rare, have never been analyzed collectively. To bridge this gap, we developed an extensive database encompassing all published and unpublished cases of POLR3-RDs and conducted the first comprehensive genotype-phenotype correlation study across their entire spectrum. This work contributed new cases, representing 13% of all documented cases in the literature, along with 31 novel variants, accounting for 8% of all identified variants. This database was constructed by systematically reviewing the literature and integrating data from patients under the care of our international network of collaborators. The dataset includes genotype curation, bioinformatics, prior publications, and individual patient outcome information. By leveraging these comprehensive data, we were able to establish clear genotype-phenotype correlations for some pathogenic variants, which will help provide optimal clinical care and genetic counseling (including insights into disease phenotypes and progression) and offer valuable guidance for future clinical trial design and patient stratification.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":" ","pages":"100481"},"PeriodicalIF":3.6,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12391809/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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